DNA metabarcoding of hidden biodiversity in the Mediterranean Basin

Abstract

One of the most remarkable features of Mediterranean-type regions worldwide is their high levels of biodiversity. However, it is striking that we still know so little about many of its taxa, particularly regarding the invertebrates. This is regrettable, because Mediterranean biodiversity is threatened by a range of factors that include land use changes, overexploitation of natural resources and global climate changes. As a consequence, biodiversity assessments and biomonitoring studies are more urgent than ever, as they provide critical baselines for planning and monitoring conservation programs. For many species groups, key obstacles to the development of comprehensive biodiversity surveys are the shortage of specialised taxonomists, and the fact that “traditional” taxonomic work is highly time consuming. Furthermore, there is increasing evidence that many species recognised based only on morphology are indeed complexes of cryptic species, which adds difficulty to “traditional” taxonomy. Until recently, these difficulties seemed largely unsurmountable, and thus conservation research has mainly focused on a narrow set of taxonomic groups such as vertebrates or flowering plants, or otherwise on a few charismatic species of arthropods or of other less known groups. Fortunately, the situation is changing fast, due to the advent of next-generation sequencing coupled with DNA metabarcoding approaches. These powerful tools have the ability to revolutionise biodiversity research in the Mediterranean, making it possible to survey virtually any group of species, with highly replicated sampling, at a range of spatial and temporal scales. In this presentation, we provide an overview of DNA metabarcoding for conservation research in the Mediterranean, using a case study in NE Portugal where we are evaluating the complementarity of natural and agricultural habitats for nocturnal arthropods assemblages. First, we illustrate the development of a comprehensive DNA barcode collection of target taxonomic groups, which is a critical prerequisite for developing conservation research using DNA metabarcoding. In particular, we highlight the role of “traditional” taxonomists, which need to remain deeply involved despite the development of molecular techniques. Second, we illustrate how samples can be collected and processed to allow for DNA metabarcoding studies, and stress the importance of robust and highly-replicated sampling designs. Third, we describe the lab and bioinformatics pipelines, providing a simple overview on the challenges and potential pitfalls. Fourth, we show the type of data that emerges from DNA metabarcoding studies, and how they can be used to answer conservation biology questions. Finally, we end with a quick overview on the potential and current limitations for mainstreaming DNA metabarcoding into Mediterranean conservation research.